Biocview "Transcriptomics"

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

Adaptive Dropout Imputer (ADImpute)

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

An alignment and integration method for single cell genomics

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis of Transposable Elements

Analyze Transcription Factor Enrichment

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

A search tool for single cell RNA-seq data by gene lists

askoR - Differential Expresion Analysis using edgeR

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Asymmetric Within-Sample Transformation

A Tidy Transcriptomics introduction to RNA-Seq analyses

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

A Tool for Generic Cell Type Enrichment Analysis

A tool for unsupervised projection of single cell RNA-seq data

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Automated functions for comparing various omic data from cbioportal.org

Automated, probabilistic assignment of scRNA-seq to cell types

Base NanoString Experiment Class

Bayesian Analysis of Single-Cell Sequencing data

BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Calculate JCC Scores

Cancer Clone Finder

Casc

Causal network analysis methods

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

Cell-Cycle using Mixture Models

CellRanger Input/Output

Classify Samples From RNA-Seq Datasets

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Clone Identification from Single Cell Data

Cluster analysis of Spatial Transcriptomics data

Clustering Algorithms for Bioconductor

Clustering and Resolution Enhancement of Spatial Transcriptomes

Co-expression Modules identification Tool

COexpression Tables ANalysis

Comparative Evaluation and Visualization of Differential Expression Analyses

Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Compendium of human transcriptome sequences

Computational pipeline for computing probability of modification from structure probing experiment data

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Controlling bias and inflation in association studies using the empirical null distribution

Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

COSMOS (Causal Oriented Search of Multi-Omic Space)

Covariate Assisted Large-scale Multiple testing

Cross omic genetic fingerprinting

Data-driven Annotation of the Transcriptome

Data normalization by matrix raking

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Deconvolution of Expression for Nascent RNA Sequencing Data

Deconvolution of mixed cells from spatial and/or bulk gene expression data

Delineate outstanding genomic zones of differential gene activity

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Detecting abberant splicing events from RNA-sequencing data

Determination of essential phenotypic elements of clusters in high-dimensional entities

Differential Alternative Polyadenylation Analysis From Compositions

Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Differentially Expressed Gene-Gene pairs

Differential Topology, Progression and Differentiation.

Diffusion scores on biological networks

Discriminant Analysis for Evolutionary Inference

Empirical Analysis of Digital Gene Expression Data in R

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Estimate Promoter Activity from RNA-Seq data

Estimates Isoform Specific RPF Footprint Densities

Evaluate Cellspecific Mixing

Exon-Intron Split Analysis (EISA) in R

explore metrics for sample annotation for genomic experiments

Exposome and omic data associatin and integration analysis

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

FCBF-based Co-Expression Networks for Single Cells

Filtering of Lowly Expressed Features

Fit Penalised Generalised Least Squares models

Functional interpretation of single cell RNA-seq latent manifolds

Gene expression-based subtype classification for high-grade serous ovarian cancer

Gene expression changes in three biological conditions

Gene Expression Meta-analysis Visualization Tool

Gene Expression Variation Analysis (GEVA)

Gene regulator enrichment analysis

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Genetic inteRaction and EssenTiality neTwork mApper

GEOexplorer: a webserver for gene expression analysis and visualisation

Global Test for Counts

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation

Helper Functions for LIBD Deconvolution

Higher-Order Deconvolution Survival Analyses

Identification of candidate causal perturbations from differential gene expression data

Identifies differentially expressed genes with respect to other local genes

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Identify Different Architectures of Sequence Elements

Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Improving replicability in single-cell RNA-Seq cell type discovery

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Inference of gene regulatory networks from gene expression data

Inferring the Tree of Cells

Infers biological signatures from gene expression data

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

Integrating Cap Enrichment with Transcript Expression Analysis

Integrating SpatialExperiment with Simple Features in sf

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

interactive analysis and visualization of alternative splicing in R

Interactive SummarizedExperiment Explorer

Interactive visualization of scRNA-seq data with Cerebro

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Interspecies gene mapping

Introduction to Tidy Transcriptomics

iSEE Universe

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Landscape Single Cell Entropy

Learn and Apply Cell Type Signatures

Linear Models for Microarray Data

Log Fold Change Distribution Tools for Working with Ratios of Counts

Long gene expression as a metric for neuronal identity

Mapping Alternative Splicing Events to pRoteins

Maximum Likelihood Decay Modeling of RNA Degradation Data

Mean Alterations Using Discrete Expression

megadepth: BigWig and BAM related utilities

Methods for analyzing spatially resolved transcriptomics data

Methods for Single-Cell RNA-Seq Data Analysis

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Mini-batch K-means Clustering for Single-Cell RNA-seq

Minimized Single-Cell Consensus Clustering

MLG Clustering

Model-based Analysis of Single Cell Transcriptomics

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

Multi-Contrast Gene Set Enrichment Analysis

Multi Omic Master Regulator Analysis

Multivariate analysis of microarray data using ADE4

NanoString data normalization and differential gene expression analysis

NanoString GeoMx Tools

NanoString nCounter Tools

Negative binomial model for scRNA-seq

Network Analysis Supported by Boosting

Network Perturbation Amplitude

Network smoothing for scRNAseq

NEUral network-based single-Cell Annotation tool

Normalization of Single-Cell mRNA Sequencing Data

Object design (S4) for AMARETTO

Omics Longitudinal Differential Analysis

OmniPath web service client and more

ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Optimising the Definition of Expressed Regions

Outlier Analysis for pairwise differential comparison

Outlier-aware and Count-based Compositional Analysis of Single-cell Data.

OUTRIDER - OUTlier in RNA-Seq fInDER

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Perform co-DE gene analysis

Phenotypic EMD for comparison of single-cell samples

pipeComp pipeline benchmarking framework

Pipeline for augmented co-expression analysis

Pipelines for Bi-Clustering Using Matrix Factorization

Plots and annotation for choosing BrainFlow target probe sequence

PolyA counting and differential transcript usage analysis for scRNA-seq data

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

Programmatic access to the DEE2 RNA expression dataset

Quality Control for Single-Cell RNA-seq Data

Quality Control of Normalized Gene Expression Data

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Rank-based signature enrichment analysis for single-cell data

RcisTarget: Identify transcription factor binding motifs enriched on a gene list

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Reference-Based Single-Cell RNA-Seq Annotation

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Retrieves Condition-Specific Variants in RNA-Seq Data

RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

RLSeq: An analysis package for R-loop mapping data

RNA Centric Annotation System

RNA-seq analysis using multiple algorithms

R package for RIVER (RNA-Informed Variant Effect on Regulation)

R wrapper for SpatialDE

S4 Class for Spatially Resolved -omics Data

SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Scaling normalization based on the Pareto distribution

SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

scMerge: Merging multiple batches of scRNA-seq data

scReClassify: post hoc cell type classification of single-cell RNA-seq data

scRecover for imputation of single-cell RNA-seq data

Selecting transcript model using PRO-seq

Shiny-based interactive data-quality exploration for omics data

Signature-based Clustering for Diagnostic Purposes

Signature discovery from omics data

Simple Simulation of Single-cell RNA Sequencing Data

Simulation and Deconvolution of Omic Profiles

Single-cell analysis toolkit for gene expression data in R

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single-Cell Batch Correction Methods

Single-Cell Consensus Clustering

Single Cell Entropy

single-cell higher order testing

Single Cell Overview of Normalized Expression data

Single cell replicability analysis

Single-Cell RNA-Seq Analysis Utilities

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Single-cell Targetted Network Inference

Single-Cell UTR Bootstrap Tools

Small-Count Analysis Methods for High-Dimensional Data

SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection

Sparse Partial Correlations On Gene Expression

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial Reconstruction of Tissues from scRNA-seq Data

Spatial transcriptome analyses of Nanostring's DSP data in R

Spatial Transcriptomics Analysis

Splicing Diversity Analysis for Transcriptome Data

SpotClean adjusts for spot swapping in spatial transcriptomics data

ssPATHS: Single Sample PATHway Score

Standardize Antibody Names

Stan implementation of BASiCS

stJoincount - Join count statistic for quantifying spatial correlation between clusters

Structure Learning for Count Data

Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Switch-like differential expression across single-cell trajectories

text mining for msigdb sets construed as documents

TFutils

the R package for analyzing expression evolution based on RNA-seq data

The scigenex package (Single-Cell Informative GENe Explorer)

The tidyomics blog

Tidy Meta Profiles using Bioconductor and the Tidyverse

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Tidyverse functions for SummarizedExperiment

Tomo-seq data analysis

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for ordering single-cell sequencing

Tools for spliced gene structure manipulation and analysis

Tools to work with a Compendium of 181000 human transcriptome sequencing studies

Top Confident Effect Sizes

trajectory-based differential expression analysis for sequencing data

Trajectory functions for visualization and interpretation.

Transcriptional Data Guided fMRI Network Classification

Transcriptome CUTteR

Transcript Quantification Import with Automatic Metadata

Translational control assessment from ribosome footprint and total RNA libraries

tricycle: Transferable Representation and Inference of cell cycle

TSS sequencing data analysis

Unified Statistical Modeling of Omics Data

Unlocking iSEE for transcript-level visualization

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Utilities for Handling Single-Cell Droplet Data

Varying-Censoring Aware Matrix Factorization

VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

Visual and interactive gene expression analysis

Visual Exploration of Omic Datasets Using a Shiny App

Visualization functions for spatial transcriptomics data

Weighting protein-protein interactions

What the Package Does TODOELI

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "Transcriptomics"

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